Open Source Software
Members of the CRC already use and actively contribute to the following Open Source projects as part of their research
Current projects:
- Berkeley Advanced Reconstruction Toolbox for computational MRI (M. Uecker, main author) [Zenodo]
- Netgen/NGSolve high performance finite element library (C. Lehrenfeld) [Homepage]
- ProxToolbox nonlinear optimization toolbox (R. Luke, main author) [Homepage]
- GROMACS molecular dynamics project (H. Grubmüller and B. L. de Groot) [Homepage]
- Transport R package for optimal transport (B. Schmitzer) [Homepage]
- Otinference R package for inference for optimal transport (A. Munk) [Homepage]
- MultiScaleOT numerical optimal transport library (B. Schmitzer, main author) [Github]
- regpy Python package for inverse problems (T. Hohage, C. Lehrenfeld, C. Rügge, M.Uecker) [Github]
- HoloTomoToolbox Matlab toolbox for holographic tomography (T. Salditt) [Github]
- Snip - Digital Labbook (M. Osterhoff) [Gitlab]
- NeuralPredictors, a library for predicting neuronal responses (F. Sinz) [Github]
- A library for computing Most Exciting Images for neurons (F. Sinz) [Github]
- NNFabrik a library for automating large scale model training for neuroscience and beyond (F. Sinz) [Github]
- ART-MOKE: Simulation and Analysis Tools for Angle-Resolved Transverse Magneto-Optical Kerr Effect Spectroscopy (M. Jansen) [Dataverse]
- De novo Structural Ensemble Determination from Single Molecule X-ray Scattering using a Bayesian Approach (H. Grubmüller) [Gitlab]
- Linearized optimal transport toolbox for Python (B. Schmitzer) [Gitlab]
- MultiMatch package for colocalization analysis of chain-like structures (G. Nies) [Gitlab]
- SimSpec (A. Kehl, H. Wiechers, M. Bennati and Y. Pokern) [Dataverse]
- Sensorium Competition for benchmarking predictive models of the brain (A. Ecker, F. Sinz) [Homepage, Github]
- MuSink (G. Mordant, T. Staudt) [Gitlab]
Former projects:
- DataJoint framework for scientific databases and data pipelines (A. Ecker) [Homepage]
- FDRSeg R package for estimation of step functions (H. Li, main author) [Homepage]